From 2317cd5cdca642fba5f14fd59355d3aae4ee3441 Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" <41898282+github-actions[bot]@users.noreply.github.com> Date: Thu, 8 Aug 2024 08:54:08 +0200 Subject: [PATCH] Release version 3.1.2 (#149) * Version 3.1.2 * improved installation process * minor edits in the github workflows * minor edits in the JOSS paper --------- Co-authored-by: Jonas I. Liechti --- DESCRIPTION | 4 +- NEWS.md | 11 +++ README.md | 8 +- configure | 272 ++++++++++++++++++++++++++------------------------- configure.ac | 2 +- 5 files changed, 157 insertions(+), 140 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index b7cd02393..0790120ab 100755 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: abn Title: Modelling Multivariate Data with Additive Bayesian Networks -Version: 3.1.1 -Date: 2024-05-22 +Version: 3.1.2 +Date: 2024-08-07 Authors@R: c( person("Matteo", "Delucchi", , "matteo.delucchi@math.uzh.ch", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-9327-1496")), diff --git a/NEWS.md b/NEWS.md index 9b9304270..13d893ec8 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,15 @@ +# abn 3.1.2 +[diff](https://github.com/furrer-lab/abn/compare/3.1.1...3.1.2) + +> 2024-08-07 + +### Fix + +* Simplified installation process ([#143](https://github.com/furrer-lab/abn/issues/143), [#142](https://github.com/furrer-lab/abn/issues/142), [#141](https://github.com/furrer-lab/abn/issues/141), [#125](https://github.com/furrer-lab/abn/issues/125), [#124](https://github.com/furrer-lab/abn/issues/124), [#123](https://github.com/furrer-lab/abn/issues/123), [#117](https://github.com/furrer-lab/abn/issues/117), [#114](https://github.com/furrer-lab/abn/issues/114)) +* Minor fixes in JOSS paper ([#147](https://github.com/furrer-lab/abn/issues/147), [#129](https://github.com/furrer-lab/abn/issues/129)) +* Some fixes and improvements in automation pipelines ([#140](https://github.com/furrer-lab/abn/issues/140), [#138](https://github.com/furrer-lab/abn/issues/138), [#132](https://github.com/furrer-lab/abn/issues/132), [#127](https://github.com/furrer-lab/abn/issues/127), [#111](https://github.com/furrer-lab/abn/issues/111)) + # abn 3.1.1 [diff](https://github.com/furrer-lab/abn/compare/3.1.0...3.1.1) diff --git a/README.md b/README.md index d526d51e6..f1e531fea 100644 --- a/README.md +++ b/README.md @@ -5,7 +5,7 @@ [![status](https://joss.theoj.org/papers/1bbc43a2be86f5d3f831cedb5cf81812/status.svg)](https://joss.theoj.org/papers/1bbc43a2be86f5d3f831cedb5cf81812) -[![On Label CRAN Checks](https://github.com/furrer-lab/abn/actions/workflows/onlabel_CRAN_checks.yml/badge.svg?branch=release-3.1.1)](https://github.com/furrer-lab/abn/actions/workflows/onlabel_CRAN_checks.yml) +[![On Label CRAN Checks](https://github.com/furrer-lab/abn/actions/workflows/onlabel_CRAN_checks.yml/badge.svg?branch=release-3.1.2)](https://github.com/furrer-lab/abn/actions/workflows/onlabel_CRAN_checks.yml) [![Codecov](https://img.shields.io/codecov/c/github/furrer-lab/abn)](https://app.codecov.io/gh/furrer-lab/abn) [![GitHub R package version](https://img.shields.io/github/r-package/v/furrer-lab/abn)](https://github.com/furrer-lab/abn/tags) ![cran](https://www.r-pkg.org/badges/version-ago/abn) @@ -315,7 +315,7 @@ install.packages('pak', repos=c(CRAN="https://cran.r-project.org")) To install `abn` run in your R session: ```R -pak::repo_add(INLA = "https://inla.r-inla-download.org/R/stable/") +pak::repo_add(INLA = "https://inla.r-inla-download.org/R/stable/") pak::pkg_install("furrer-lab/abn@3.1.1", dependencies=TRUE) ``` _**Note:** The first command can be skipped on MacOS or Windows._ @@ -329,8 +329,10 @@ _**Note:** The first command can be skipped on MacOS or Windows._ In order to install the `abn` version on CRAN, open an R session and type: ```R +pak::repo_add(INLA = "https://inla.r-inla-download.org/R/stable/") pak::pkg_install("abn", dependencies=TRUE) ``` +_**Note:** The first command can be skipped on MacOS or Windows._ `abn` has several dependencies that are not available on CRAN. This is why we rely on [pak](https://pak.r-lib.org/) for the installation and the [Prior to installing](#prior-to-installing) section should be followed through before installing `abn` from CRAN. [^1] @@ -366,7 +368,7 @@ Installing from source is done with the following steps: 3. Build and install the local content with dependencies: ```R - pak::repo_add(INLA = "https://inla.r-inla-download.org/R/stable/") + pak::repo_add(INLA = "https://inla.r-inla-download.org/R/stable/") pak::local_install(dependencies=TRUE) ``` _**Note:** The first command can be skipped on MacOS or Windows._ diff --git a/configure b/configure index 5efade7cb..f15b15deb 100755 --- a/configure +++ b/configure @@ -1,9 +1,9 @@ #! /bin/sh # Guess values for system-dependent variables and create Makefiles. -# Generated by GNU Autoconf 2.72 for abn 3.1.1. +# Generated by GNU Autoconf 2.71 for abn 3.1.2. # # -# Copyright (C) 1992-1996, 1998-2017, 2020-2023 Free Software Foundation, +# Copyright (C) 1992-1996, 1998-2017, 2020-2021 Free Software Foundation, # Inc. # # @@ -15,6 +15,7 @@ # Be more Bourne compatible DUALCASE=1; export DUALCASE # for MKS sh +as_nop=: if test ${ZSH_VERSION+y} && (emulate sh) >/dev/null 2>&1 then : emulate sh @@ -23,13 +24,12 @@ then : # is contrary to our usage. Disable this feature. alias -g '${1+"$@"}'='"$@"' setopt NO_GLOB_SUBST -else case e in #( - e) case `(set -o) 2>/dev/null` in #( +else $as_nop + case `(set -o) 2>/dev/null` in #( *posix*) : set -o posix ;; #( *) : ;; -esac ;; esac fi @@ -101,7 +101,7 @@ IFS=$as_save_IFS ;; esac -# We did not find ourselves, most probably we were run as 'sh COMMAND' +# We did not find ourselves, most probably we were run as `sh COMMAND' # in which case we are not to be found in the path. if test "x$as_myself" = x; then as_myself=$0 @@ -131,14 +131,15 @@ case $- in # (((( esac exec $CONFIG_SHELL $as_opts "$as_myself" ${1+"$@"} # Admittedly, this is quite paranoid, since all the known shells bail -# out after a failed 'exec'. +# out after a failed `exec'. printf "%s\n" "$0: could not re-execute with $CONFIG_SHELL" >&2 exit 255 fi # We don't want this to propagate to other subprocesses. { _as_can_reexec=; unset _as_can_reexec;} if test "x$CONFIG_SHELL" = x; then - as_bourne_compatible="if test \${ZSH_VERSION+y} && (emulate sh) >/dev/null 2>&1 + as_bourne_compatible="as_nop=: +if test \${ZSH_VERSION+y} && (emulate sh) >/dev/null 2>&1 then : emulate sh NULLCMD=: @@ -146,13 +147,12 @@ then : # is contrary to our usage. Disable this feature. alias -g '\${1+\"\$@\"}'='\"\$@\"' setopt NO_GLOB_SUBST -else case e in #( - e) case \`(set -o) 2>/dev/null\` in #( +else \$as_nop + case \`(set -o) 2>/dev/null\` in #( *posix*) : set -o posix ;; #( *) : ;; -esac ;; esac fi " @@ -170,9 +170,8 @@ as_fn_ret_failure && { exitcode=1; echo as_fn_ret_failure succeeded.; } if ( set x; as_fn_ret_success y && test x = \"\$1\" ) then : -else case e in #( - e) exitcode=1; echo positional parameters were not saved. ;; -esac +else \$as_nop + exitcode=1; echo positional parameters were not saved. fi test x\$exitcode = x0 || exit 1 blah=\$(echo \$(echo blah)) @@ -185,15 +184,14 @@ test -x / || exit 1" if (eval "$as_required") 2>/dev/null then : as_have_required=yes -else case e in #( - e) as_have_required=no ;; -esac +else $as_nop + as_have_required=no fi if test x$as_have_required = xyes && (eval "$as_suggested") 2>/dev/null then : -else case e in #( - e) as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +else $as_nop + as_save_IFS=$IFS; IFS=$PATH_SEPARATOR as_found=false for as_dir in /bin$PATH_SEPARATOR/usr/bin$PATH_SEPARATOR$PATH do @@ -226,13 +224,12 @@ IFS=$as_save_IFS if $as_found then : -else case e in #( - e) if { test -f "$SHELL" || test -f "$SHELL.exe"; } && +else $as_nop + if { test -f "$SHELL" || test -f "$SHELL.exe"; } && as_run=a "$SHELL" -c "$as_bourne_compatible""$as_required" 2>/dev/null then : CONFIG_SHELL=$SHELL as_have_required=yes -fi ;; -esac +fi fi @@ -254,7 +251,7 @@ case $- in # (((( esac exec $CONFIG_SHELL $as_opts "$as_myself" ${1+"$@"} # Admittedly, this is quite paranoid, since all the known shells bail -# out after a failed 'exec'. +# out after a failed `exec'. printf "%s\n" "$0: could not re-execute with $CONFIG_SHELL" >&2 exit 255 fi @@ -273,8 +270,7 @@ $0: message. Then install a modern shell, or manually run $0: the script under such a shell if you do have one." fi exit 1 -fi ;; -esac +fi fi fi SHELL=${CONFIG_SHELL-/bin/sh} @@ -313,6 +309,14 @@ as_fn_exit () as_fn_set_status $1 exit $1 } # as_fn_exit +# as_fn_nop +# --------- +# Do nothing but, unlike ":", preserve the value of $?. +as_fn_nop () +{ + return $? +} +as_nop=as_fn_nop # as_fn_mkdir_p # ------------- @@ -381,12 +385,11 @@ then : { eval $1+=\$2 }' -else case e in #( - e) as_fn_append () +else $as_nop + as_fn_append () { eval $1=\$$1\$2 - } ;; -esac + } fi # as_fn_append # as_fn_arith ARG... @@ -400,14 +403,21 @@ then : { as_val=$(( $* )) }' -else case e in #( - e) as_fn_arith () +else $as_nop + as_fn_arith () { as_val=`expr "$@" || test $? -eq 1` - } ;; -esac + } fi # as_fn_arith +# as_fn_nop +# --------- +# Do nothing but, unlike ":", preserve the value of $?. +as_fn_nop () +{ + return $? +} +as_nop=as_fn_nop # as_fn_error STATUS ERROR [LINENO LOG_FD] # ---------------------------------------- @@ -481,8 +491,6 @@ as_cr_alnum=$as_cr_Letters$as_cr_digits /[$]LINENO/= ' <$as_myself | sed ' - t clear - :clear s/[$]LINENO.*/&-/ t lineno b @@ -531,6 +539,7 @@ esac as_echo='printf %s\n' as_echo_n='printf %s' + rm -f conf$$ conf$$.exe conf$$.file if test -d conf$$.dir; then rm -f conf$$.dir/conf$$.file @@ -542,9 +551,9 @@ if (echo >conf$$.file) 2>/dev/null; then if ln -s conf$$.file conf$$ 2>/dev/null; then as_ln_s='ln -s' # ... but there are two gotchas: - # 1) On MSYS, both 'ln -s file dir' and 'ln file dir' fail. - # 2) DJGPP < 2.04 has no symlinks; 'ln -s' creates a wrapper executable. - # In both cases, we have to default to 'cp -pR'. + # 1) On MSYS, both `ln -s file dir' and `ln file dir' fail. + # 2) DJGPP < 2.04 has no symlinks; `ln -s' creates a wrapper executable. + # In both cases, we have to default to `cp -pR'. ln -s conf$$.file conf$$.dir 2>/dev/null && test ! -f conf$$.exe || as_ln_s='cp -pR' elif ln conf$$.file conf$$ 2>/dev/null; then @@ -569,12 +578,10 @@ as_test_x='test -x' as_executable_p=as_fn_executable_p # Sed expression to map a string onto a valid CPP name. -as_sed_cpp="y%*$as_cr_letters%P$as_cr_LETTERS%;s%[^_$as_cr_alnum]%_%g" -as_tr_cpp="eval sed '$as_sed_cpp'" # deprecated +as_tr_cpp="eval sed 'y%*$as_cr_letters%P$as_cr_LETTERS%;s%[^_$as_cr_alnum]%_%g'" # Sed expression to map a string onto a valid variable name. -as_sed_sh="y%*+%pp%;s%[^_$as_cr_alnum]%_%g" -as_tr_sh="eval sed '$as_sed_sh'" # deprecated +as_tr_sh="eval sed 'y%*+%pp%;s%[^_$as_cr_alnum]%_%g'" test -n "$DJDIR" || exec 7<&0 /dev/null && - as_fn_error $? "invalid feature name: '$ac_useropt'" + as_fn_error $? "invalid feature name: \`$ac_useropt'" ac_useropt_orig=$ac_useropt ac_useropt=`printf "%s\n" "$ac_useropt" | sed 's/[-+.]/_/g'` case $ac_user_opts in @@ -791,7 +798,7 @@ do ac_useropt=`expr "x$ac_option" : 'x-*enable-\([^=]*\)'` # Reject names that are not valid shell variable names. expr "x$ac_useropt" : ".*[^-+._$as_cr_alnum]" >/dev/null && - as_fn_error $? "invalid feature name: '$ac_useropt'" + as_fn_error $? "invalid feature name: \`$ac_useropt'" ac_useropt_orig=$ac_useropt ac_useropt=`printf "%s\n" "$ac_useropt" | sed 's/[-+.]/_/g'` case $ac_user_opts in @@ -1004,7 +1011,7 @@ do ac_useropt=`expr "x$ac_option" : 'x-*with-\([^=]*\)'` # Reject names that are not valid shell variable names. expr "x$ac_useropt" : ".*[^-+._$as_cr_alnum]" >/dev/null && - as_fn_error $? "invalid package name: '$ac_useropt'" + as_fn_error $? "invalid package name: \`$ac_useropt'" ac_useropt_orig=$ac_useropt ac_useropt=`printf "%s\n" "$ac_useropt" | sed 's/[-+.]/_/g'` case $ac_user_opts in @@ -1020,7 +1027,7 @@ do ac_useropt=`expr "x$ac_option" : 'x-*without-\(.*\)'` # Reject names that are not valid shell variable names. expr "x$ac_useropt" : ".*[^-+._$as_cr_alnum]" >/dev/null && - as_fn_error $? "invalid package name: '$ac_useropt'" + as_fn_error $? "invalid package name: \`$ac_useropt'" ac_useropt_orig=$ac_useropt ac_useropt=`printf "%s\n" "$ac_useropt" | sed 's/[-+.]/_/g'` case $ac_user_opts in @@ -1050,8 +1057,8 @@ do | --x-librar=* | --x-libra=* | --x-libr=* | --x-lib=* | --x-li=* | --x-l=*) x_libraries=$ac_optarg ;; - -*) as_fn_error $? "unrecognized option: '$ac_option' -Try '$0 --help' for more information" + -*) as_fn_error $? "unrecognized option: \`$ac_option' +Try \`$0 --help' for more information" ;; *=*) @@ -1059,7 +1066,7 @@ Try '$0 --help' for more information" # Reject names that are not valid shell variable names. case $ac_envvar in #( '' | [0-9]* | *[!_$as_cr_alnum]* ) - as_fn_error $? "invalid variable name: '$ac_envvar'" ;; + as_fn_error $? "invalid variable name: \`$ac_envvar'" ;; esac eval $ac_envvar=\$ac_optarg export $ac_envvar ;; @@ -1109,7 +1116,7 @@ do as_fn_error $? "expected an absolute directory name for --$ac_var: $ac_val" done -# There might be people who depend on the old broken behavior: '$host' +# There might be people who depend on the old broken behavior: `$host' # used to hold the argument of --host etc. # FIXME: To remove some day. build=$build_alias @@ -1177,7 +1184,7 @@ if test ! -r "$srcdir/$ac_unique_file"; then test "$ac_srcdir_defaulted" = yes && srcdir="$ac_confdir or .." as_fn_error $? "cannot find sources ($ac_unique_file) in $srcdir" fi -ac_msg="sources are in $srcdir, but 'cd $srcdir' does not work" +ac_msg="sources are in $srcdir, but \`cd $srcdir' does not work" ac_abs_confdir=`( cd "$srcdir" && test -r "./$ac_unique_file" || as_fn_error $? "$ac_msg" pwd)` @@ -1205,7 +1212,7 @@ if test "$ac_init_help" = "long"; then # Omit some internal or obsolete options to make the list less imposing. # This message is too long to be a string in the A/UX 3.1 sh. cat <<_ACEOF -'configure' configures abn 3.1.1 to adapt to many kinds of systems. +\`configure' configures abn 3.1.2 to adapt to many kinds of systems. Usage: $0 [OPTION]... [VAR=VALUE]... @@ -1219,11 +1226,11 @@ Configuration: --help=short display options specific to this package --help=recursive display the short help of all the included packages -V, --version display version information and exit - -q, --quiet, --silent do not print 'checking ...' messages + -q, --quiet, --silent do not print \`checking ...' messages --cache-file=FILE cache test results in FILE [disabled] - -C, --config-cache alias for '--cache-file=config.cache' + -C, --config-cache alias for \`--cache-file=config.cache' -n, --no-create do not create output files - --srcdir=DIR find the sources in DIR [configure dir or '..'] + --srcdir=DIR find the sources in DIR [configure dir or \`..'] Installation directories: --prefix=PREFIX install architecture-independent files in PREFIX @@ -1231,10 +1238,10 @@ Installation directories: --exec-prefix=EPREFIX install architecture-dependent files in EPREFIX [PREFIX] -By default, 'make install' will install all the files in -'$ac_default_prefix/bin', '$ac_default_prefix/lib' etc. You can specify -an installation prefix other than '$ac_default_prefix' using '--prefix', -for instance '--prefix=\$HOME'. +By default, \`make install' will install all the files in +\`$ac_default_prefix/bin', \`$ac_default_prefix/lib' etc. You can specify +an installation prefix other than \`$ac_default_prefix' using \`--prefix', +for instance \`--prefix=\$HOME'. For better control, use the options below. @@ -1267,7 +1274,7 @@ fi if test -n "$ac_init_help"; then case $ac_init_help in - short | recursive ) echo "Configuration of abn 3.1.1:";; + short | recursive ) echo "Configuration of abn 3.1.2:";; esac cat <<\_ACEOF @@ -1335,10 +1342,10 @@ fi test -n "$ac_init_help" && exit $ac_status if $ac_init_version; then cat <<\_ACEOF -abn configure 3.1.1 -generated by GNU Autoconf 2.72 +abn configure 3.1.2 +generated by GNU Autoconf 2.71 -Copyright (C) 2023 Free Software Foundation, Inc. +Copyright (C) 2021 Free Software Foundation, Inc. This configure script is free software; the Free Software Foundation gives unlimited permission to copy, distribute and modify it. _ACEOF @@ -1372,8 +1379,8 @@ cat >config.log <<_ACEOF This file contains any messages produced by compilers while running configure, to aid debugging if configure makes a mistake. -It was created by abn $as_me 3.1.1, which was -generated by GNU Autoconf 2.72. Invocation command line was +It was created by abn $as_me 3.1.2, which was +generated by GNU Autoconf 2.71. Invocation command line was $ $0$ac_configure_args_raw @@ -1619,10 +1626,10 @@ esac printf "%s\n" "$as_me: loading site script $ac_site_file" >&6;} sed 's/^/| /' "$ac_site_file" >&5 . "$ac_site_file" \ - || { { printf "%s\n" "$as_me:${as_lineno-$LINENO}: error: in '$ac_pwd':" >&5 -printf "%s\n" "$as_me: error: in '$ac_pwd':" >&2;} + || { { printf "%s\n" "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5 +printf "%s\n" "$as_me: error: in \`$ac_pwd':" >&2;} as_fn_error $? "failed to load site script $ac_site_file -See 'config.log' for more details" "$LINENO" 5; } +See \`config.log' for more details" "$LINENO" 5; } fi done @@ -1653,12 +1660,12 @@ for ac_var in $ac_precious_vars; do eval ac_new_val=\$ac_env_${ac_var}_value case $ac_old_set,$ac_new_set in set,) - { printf "%s\n" "$as_me:${as_lineno-$LINENO}: error: '$ac_var' was set to '$ac_old_val' in the previous run" >&5 -printf "%s\n" "$as_me: error: '$ac_var' was set to '$ac_old_val' in the previous run" >&2;} + { printf "%s\n" "$as_me:${as_lineno-$LINENO}: error: \`$ac_var' was set to \`$ac_old_val' in the previous run" >&5 +printf "%s\n" "$as_me: error: \`$ac_var' was set to \`$ac_old_val' in the previous run" >&2;} ac_cache_corrupted=: ;; ,set) - { printf "%s\n" "$as_me:${as_lineno-$LINENO}: error: '$ac_var' was not set in the previous run" >&5 -printf "%s\n" "$as_me: error: '$ac_var' was not set in the previous run" >&2;} + { printf "%s\n" "$as_me:${as_lineno-$LINENO}: error: \`$ac_var' was not set in the previous run" >&5 +printf "%s\n" "$as_me: error: \`$ac_var' was not set in the previous run" >&2;} ac_cache_corrupted=: ;; ,);; *) @@ -1667,18 +1674,18 @@ printf "%s\n" "$as_me: error: '$ac_var' was not set in the previous run" >&2;} ac_old_val_w=`echo x $ac_old_val` ac_new_val_w=`echo x $ac_new_val` if test "$ac_old_val_w" != "$ac_new_val_w"; then - { printf "%s\n" "$as_me:${as_lineno-$LINENO}: error: '$ac_var' has changed since the previous run:" >&5 -printf "%s\n" "$as_me: error: '$ac_var' has changed since the previous run:" >&2;} + { printf "%s\n" "$as_me:${as_lineno-$LINENO}: error: \`$ac_var' has changed since the previous run:" >&5 +printf "%s\n" "$as_me: error: \`$ac_var' has changed since the previous run:" >&2;} ac_cache_corrupted=: else - { printf "%s\n" "$as_me:${as_lineno-$LINENO}: warning: ignoring whitespace changes in '$ac_var' since the previous run:" >&5 -printf "%s\n" "$as_me: warning: ignoring whitespace changes in '$ac_var' since the previous run:" >&2;} + { printf "%s\n" "$as_me:${as_lineno-$LINENO}: warning: ignoring whitespace changes in \`$ac_var' since the previous run:" >&5 +printf "%s\n" "$as_me: warning: ignoring whitespace changes in \`$ac_var' since the previous run:" >&2;} eval $ac_var=\$ac_old_val fi - { printf "%s\n" "$as_me:${as_lineno-$LINENO}: former value: '$ac_old_val'" >&5 -printf "%s\n" "$as_me: former value: '$ac_old_val'" >&2;} - { printf "%s\n" "$as_me:${as_lineno-$LINENO}: current value: '$ac_new_val'" >&5 -printf "%s\n" "$as_me: current value: '$ac_new_val'" >&2;} + { printf "%s\n" "$as_me:${as_lineno-$LINENO}: former value: \`$ac_old_val'" >&5 +printf "%s\n" "$as_me: former value: \`$ac_old_val'" >&2;} + { printf "%s\n" "$as_me:${as_lineno-$LINENO}: current value: \`$ac_new_val'" >&5 +printf "%s\n" "$as_me: current value: \`$ac_new_val'" >&2;} fi;; esac # Pass precious variables to config.status. @@ -1694,11 +1701,11 @@ printf "%s\n" "$as_me: current value: '$ac_new_val'" >&2;} fi done if $ac_cache_corrupted; then - { printf "%s\n" "$as_me:${as_lineno-$LINENO}: error: in '$ac_pwd':" >&5 -printf "%s\n" "$as_me: error: in '$ac_pwd':" >&2;} + { printf "%s\n" "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5 +printf "%s\n" "$as_me: error: in \`$ac_pwd':" >&2;} { printf "%s\n" "$as_me:${as_lineno-$LINENO}: error: changes in the environment can compromise the build" >&5 printf "%s\n" "$as_me: error: changes in the environment can compromise the build" >&2;} - as_fn_error $? "run '${MAKE-make} distclean' and/or 'rm $cache_file' + as_fn_error $? "run \`${MAKE-make} distclean' and/or \`rm $cache_file' and start over" "$LINENO" 5 fi ## -------------------- ## @@ -1723,8 +1730,8 @@ printf %s "checking for $ac_word... " >&6; } if test ${ac_cv_path_GSL_CONFIG+y} then : printf %s "(cached) " >&6 -else case e in #( - e) case $GSL_CONFIG in +else $as_nop + case $GSL_CONFIG in [\\/]* | ?:[\\/]*) ac_cv_path_GSL_CONFIG="$GSL_CONFIG" # Let the user override the test with a path. ;; @@ -1749,7 +1756,6 @@ done IFS=$as_save_IFS ;; -esac ;; esac fi GSL_CONFIG=$ac_cv_path_GSL_CONFIG @@ -1783,8 +1789,8 @@ printf %s "checking for $ac_word... " >&6; } if test ${ac_cv_path_JAGS+y} then : printf %s "(cached) " >&6 -else case e in #( - e) case $JAGS in +else $as_nop + case $JAGS in [\\/]* | ?:[\\/]*) ac_cv_path_JAGS="$JAGS" # Let the user override the test with a path. ;; @@ -1809,7 +1815,6 @@ done IFS=$as_save_IFS ;; -esac ;; esac fi JAGS=$ac_cv_path_JAGS @@ -1838,8 +1843,8 @@ cat >confcache <<\_ACEOF # config.status only pays attention to the cache file if you give it # the --recheck option to rerun configure. # -# 'ac_cv_env_foo' variables (set or unset) will be overridden when -# loading this file, other *unset* 'ac_cv_foo' will be assigned the +# `ac_cv_env_foo' variables (set or unset) will be overridden when +# loading this file, other *unset* `ac_cv_foo' will be assigned the # following values. _ACEOF @@ -1869,14 +1874,14 @@ printf "%s\n" "$as_me: WARNING: cache variable $ac_var contains a newline" >&2;} (set) 2>&1 | case $as_nl`(ac_space=' '; set) 2>&1` in #( *${as_nl}ac_space=\ *) - # 'set' does not quote correctly, so add quotes: double-quote + # `set' does not quote correctly, so add quotes: double-quote # substitution turns \\\\ into \\, and sed turns \\ into \. sed -n \ "s/'/'\\\\''/g; s/^\\([_$as_cr_alnum]*_cv_[_$as_cr_alnum]*\\)=\\(.*\\)/\\1='\\2'/p" ;; #( *) - # 'set' quotes correctly as required by POSIX, so do not add quotes. + # `set' quotes correctly as required by POSIX, so do not add quotes. sed -n "/^[_$as_cr_alnum]*_cv_[_$as_cr_alnum]*=/p" ;; esac | @@ -1940,7 +1945,9 @@ s/^[ ]*#[ ]*define[ ][ ]*\([^ ][^ ]*\)[ ]*\(.*\)/-D\1=\2/g t quote b any :quote -s/[][ `~#$^&*(){}\\|;'\''"<>?]/\\&/g +s/[ `~#$^&*(){}\\|;'\''"<>?]/\\&/g +s/\[/\\&/g +s/\]/\\&/g s/\$/$$/g H :any @@ -2000,6 +2007,7 @@ cat >>$CONFIG_STATUS <<\_ASEOF || as_write_fail=1 # Be more Bourne compatible DUALCASE=1; export DUALCASE # for MKS sh +as_nop=: if test ${ZSH_VERSION+y} && (emulate sh) >/dev/null 2>&1 then : emulate sh @@ -2008,13 +2016,12 @@ then : # is contrary to our usage. Disable this feature. alias -g '${1+"$@"}'='"$@"' setopt NO_GLOB_SUBST -else case e in #( - e) case `(set -o) 2>/dev/null` in #( +else $as_nop + case `(set -o) 2>/dev/null` in #( *posix*) : set -o posix ;; #( *) : ;; -esac ;; esac fi @@ -2086,7 +2093,7 @@ IFS=$as_save_IFS ;; esac -# We did not find ourselves, most probably we were run as 'sh COMMAND' +# We did not find ourselves, most probably we were run as `sh COMMAND' # in which case we are not to be found in the path. if test "x$as_myself" = x; then as_myself=$0 @@ -2115,6 +2122,7 @@ as_fn_error () } # as_fn_error + # as_fn_set_status STATUS # ----------------------- # Set $? to STATUS, without forking. @@ -2154,12 +2162,11 @@ then : { eval $1+=\$2 }' -else case e in #( - e) as_fn_append () +else $as_nop + as_fn_append () { eval $1=\$$1\$2 - } ;; -esac + } fi # as_fn_append # as_fn_arith ARG... @@ -2173,12 +2180,11 @@ then : { as_val=$(( $* )) }' -else case e in #( - e) as_fn_arith () +else $as_nop + as_fn_arith () { as_val=`expr "$@" || test $? -eq 1` - } ;; -esac + } fi # as_fn_arith @@ -2261,9 +2267,9 @@ if (echo >conf$$.file) 2>/dev/null; then if ln -s conf$$.file conf$$ 2>/dev/null; then as_ln_s='ln -s' # ... but there are two gotchas: - # 1) On MSYS, both 'ln -s file dir' and 'ln file dir' fail. - # 2) DJGPP < 2.04 has no symlinks; 'ln -s' creates a wrapper executable. - # In both cases, we have to default to 'cp -pR'. + # 1) On MSYS, both `ln -s file dir' and `ln file dir' fail. + # 2) DJGPP < 2.04 has no symlinks; `ln -s' creates a wrapper executable. + # In both cases, we have to default to `cp -pR'. ln -s conf$$.file conf$$.dir 2>/dev/null && test ! -f conf$$.exe || as_ln_s='cp -pR' elif ln conf$$.file conf$$ 2>/dev/null; then @@ -2344,12 +2350,10 @@ as_test_x='test -x' as_executable_p=as_fn_executable_p # Sed expression to map a string onto a valid CPP name. -as_sed_cpp="y%*$as_cr_letters%P$as_cr_LETTERS%;s%[^_$as_cr_alnum]%_%g" -as_tr_cpp="eval sed '$as_sed_cpp'" # deprecated +as_tr_cpp="eval sed 'y%*$as_cr_letters%P$as_cr_LETTERS%;s%[^_$as_cr_alnum]%_%g'" # Sed expression to map a string onto a valid variable name. -as_sed_sh="y%*+%pp%;s%[^_$as_cr_alnum]%_%g" -as_tr_sh="eval sed '$as_sed_sh'" # deprecated +as_tr_sh="eval sed 'y%*+%pp%;s%[^_$as_cr_alnum]%_%g'" exec 6>&1 @@ -2364,8 +2368,8 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1 # report actual input values of CONFIG_FILES etc. instead of their # values after options handling. ac_log=" -This file was extended by abn $as_me 3.1.1, which was -generated by GNU Autoconf 2.72. Invocation command line was +This file was extended by abn $as_me 3.1.2, which was +generated by GNU Autoconf 2.71. Invocation command line was CONFIG_FILES = $CONFIG_FILES CONFIG_HEADERS = $CONFIG_HEADERS @@ -2392,7 +2396,7 @@ _ACEOF cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1 ac_cs_usage="\ -'$as_me' instantiates files and other configuration actions +\`$as_me' instantiates files and other configuration actions from templates according to the current configuration. Unless the files and actions are specified as TAGs, all are instantiated by default. @@ -2419,11 +2423,11 @@ ac_cs_config_escaped=`printf "%s\n" "$ac_cs_config" | sed "s/^ //; s/'/'\\\\\\\\ cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1 ac_cs_config='$ac_cs_config_escaped' ac_cs_version="\\ -abn config.status 3.1.1 -configured by $0, generated by GNU Autoconf 2.72, +abn config.status 3.1.2 +configured by $0, generated by GNU Autoconf 2.71, with options \\"\$ac_cs_config\\" -Copyright (C) 2023 Free Software Foundation, Inc. +Copyright (C) 2021 Free Software Foundation, Inc. This config.status script is free software; the Free Software Foundation gives unlimited permission to copy, distribute and modify it." @@ -2480,8 +2484,8 @@ do ac_cs_silent=: ;; # This is an error. - -*) as_fn_error $? "unrecognized option: '$1' -Try '$0 --help' for more information." ;; + -*) as_fn_error $? "unrecognized option: \`$1' +Try \`$0 --help' for more information." ;; *) as_fn_append ac_config_targets " $1" ac_need_defaults=false ;; @@ -2531,7 +2535,7 @@ do case $ac_config_target in "src/Makevars") CONFIG_FILES="$CONFIG_FILES src/Makevars" ;; - *) as_fn_error $? "invalid argument: '$ac_config_target'" "$LINENO" 5;; + *) as_fn_error $? "invalid argument: \`$ac_config_target'" "$LINENO" 5;; esac done @@ -2549,7 +2553,7 @@ fi # creating and moving files from /tmp can sometimes cause problems. # Hook for its removal unless debugging. # Note that there is a small window in which the directory will not be cleaned: -# after its creation but before its name has been assigned to '$tmp'. +# after its creation but before its name has been assigned to `$tmp'. $debug || { tmp= ac_tmp= @@ -2573,7 +2577,7 @@ ac_tmp=$tmp # Set up the scripts for CONFIG_FILES section. # No need to generate them if there are no CONFIG_FILES. -# This happens for instance with './config.status config.h'. +# This happens for instance with `./config.status config.h'. if test -n "$CONFIG_FILES"; then @@ -2739,7 +2743,7 @@ do esac case $ac_mode$ac_tag in :[FHL]*:*);; - :L* | :C*:*) as_fn_error $? "invalid tag '$ac_tag'" "$LINENO" 5;; + :L* | :C*:*) as_fn_error $? "invalid tag \`$ac_tag'" "$LINENO" 5;; :[FH]-) ac_tag=-:-;; :[FH]*) ac_tag=$ac_tag:$ac_tag.in;; esac @@ -2761,19 +2765,19 @@ do -) ac_f="$ac_tmp/stdin";; *) # Look for the file first in the build tree, then in the source tree # (if the path is not absolute). The absolute path cannot be DOS-style, - # because $ac_f cannot contain ':'. + # because $ac_f cannot contain `:'. test -f "$ac_f" || case $ac_f in [\\/$]*) false;; *) test -f "$srcdir/$ac_f" && ac_f="$srcdir/$ac_f";; esac || - as_fn_error 1 "cannot find input file: '$ac_f'" "$LINENO" 5;; + as_fn_error 1 "cannot find input file: \`$ac_f'" "$LINENO" 5;; esac case $ac_f in *\'*) ac_f=`printf "%s\n" "$ac_f" | sed "s/'/'\\\\\\\\''/g"`;; esac as_fn_append ac_file_inputs " '$ac_f'" done - # Let's still pretend it is 'configure' which instantiates (i.e., don't + # Let's still pretend it is `configure' which instantiates (i.e., don't # use $as_me), people would be surprised to read: # /* config.h. Generated by config.status. */ configure_input='Generated from '` @@ -2897,7 +2901,7 @@ cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1 esac _ACEOF -# Neutralize VPATH when '$srcdir' = '.'. +# Neutralize VPATH when `$srcdir' = `.'. # Shell code in configure.ac might set extrasub. # FIXME: do we really want to maintain this feature? cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1 @@ -2926,9 +2930,9 @@ test -z "$ac_datarootdir_hack$ac_datarootdir_seen" && { ac_out=`sed -n '/\${datarootdir}/p' "$ac_tmp/out"`; test -n "$ac_out"; } && { ac_out=`sed -n '/^[ ]*datarootdir[ ]*:*=/p' \ "$ac_tmp/out"`; test -z "$ac_out"; } && - { printf "%s\n" "$as_me:${as_lineno-$LINENO}: WARNING: $ac_file contains a reference to the variable 'datarootdir' + { printf "%s\n" "$as_me:${as_lineno-$LINENO}: WARNING: $ac_file contains a reference to the variable \`datarootdir' which seems to be undefined. Please make sure it is defined" >&5 -printf "%s\n" "$as_me: WARNING: $ac_file contains a reference to the variable 'datarootdir' +printf "%s\n" "$as_me: WARNING: $ac_file contains a reference to the variable \`datarootdir' which seems to be undefined. Please make sure it is defined" >&2;} rm -f "$ac_tmp/stdin" diff --git a/configure.ac b/configure.ac index e289e6412..7cf67e2ff 100644 --- a/configure.ac +++ b/configure.ac @@ -1,4 +1,4 @@ -AC_INIT([abn],[3.1.1]) +AC_INIT([abn],[3.1.2]) ## Use gsl-config to find arguments for compiler and linker flags ##